Sampling re-design increases power to detect change in the Great Barrier Reef’s inshore water quality

Monitoring programs are fundamental to understanding the state and trend of aquatic ecosystems. Sampling designs are a crucial component of monitoring programs and ensure that measurements evaluate progress toward clearly stated management objectives, which provides a mechanism for adaptive management. Here, we use a well-established marine monitoring program for inshore water quality in the Great Barrier Reef (GBR), Australia to investigate whether a sampling re-design has increased the program’s capacity to meet its primary objectives. Specifically, we use bootstrap resampling to assess the change in statistical power to detect temporal water quality trends in a 15-year inshore marine water quality data set that includes data from both before and after the sampling re-design. We perform a comprehensive power analysis for six water quality analytes at four separate study areas in the GBR Marine Park and find that the sampling re-design (i) increased power to detect trends in 23 of the 24 analyte-study area combinations, and (ii) resulted in an average increase in power of 34% to detect increasing or decreasing trends in water quality analytes. This increase in power is attributed more to the addition of sampling locations than increasing the sampling rate. Therefore, the sampling re-design has substantially increased the capacity of the program to detect temporal trends in inshore marine water quality. Further improvements in sampling design need to focus on the program’s capability to reliably detect trends within realistic timeframes where inshore improvements to water quality can be expected to occur

Mobster: Accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users

2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition, Chapter 2: sources of sediment, nutrients, pesticides and other pollutants to the Great Barrier Reef

This chapter provides an up-to-date review of the state of knowledge relating to the source of sediment and nutrients as well as pesticides and other pollutants delivered to the Great Barrier Reef from adjacent catchments. The strengths and limitations of the various datasets are also discussed. Collectively, sediment, nutrients, pesticides and other pollutants (e.g. petroleum hydrocarbons, pharmaceuticals) are described as ‘pollutants’. This chapter is focused on defining the major source areas of these pollutants across the Great Barrier Reef, how these sources have varied in space and time, the major processes (e.g. hillslope, gully and streambank erosion) delivering these pollutants, their relative loads to the Great Barrier Reef and a summary of the main drivers in terms of land use, land condition and agricultural practices. Plot- and paddock-scale studies, including the effectiveness of remediation approaches, are summarised in Chapter 4. Acknowledging that all forms of data used to estimate pollutant loads to the Great Barrier Reef have constraints and limitations, this review uses a ‘multiple lines of evidence’ approach and draws on data from three main sources. These include the Queensland Government load monitoring data, the latest Queensland Government whole of Great Barrier Reef Source Catchments modelling results (which underpin the Report Card 2015) as well as a summary of the numerous individual research projects and synthesis reports published over the last four years. Data and information are included that was published, publicly available and that had undergone a peer review process. In a few cases, grey literature (e.g. consulting reports) and journal publications currently in review are included. A synthesis of the broad findings of this chapter are outlined below and in Table 1. A detailed description of what has changed since the last Scientific Consensus Statement is provided in Table 20

Multi-modal volumetric concept activation to explain detection and classification of metastatic prostate cancer on PSMA-PET/CT

Explainable artificial intelligence (XAI) is increasingly used to analyze the behavior of neural networks. Concept activation uses human-interpretable concepts to explain neural network behavior. This study aimed at assessing the feasibility of regression concept activation to explain detection and classification of multi-modal volumetric data. Proof-of-concept was demonstrated in metastatic prostate cancer patients imaged with positron emission tomography/computed tomography (PET/CT). Multi-modal volumetric concept activation was used to provide global and local explanations. Sensitivity was 80% at 1.78 false positive per patient. Global explanations showed that detection focused on CT for anatomical location and on PET for its confidence in the detection. Local explanations showed promise to aid in distinguishing true positives from false positives. Hence, this study demonstrated feasibility to explain detection and classification of multi-modal volumetric data using regression concept activation.Comment: Accepted as: Kraaijveld, R.C.J., Philippens, M.E.P., Eppinga, W.S.C., J\"urgenliemk-Schulz, I.M., Gilhuijs, K.G.A., Kroon, P.S., van der Velden, B.H.M. "Multi-modal volumetric concept activation to explain detection and classification of metastatic prostate cancer on PSMA-PET/CT." MICCAI workshop on Interpretability of Machine Intelligence in Medical Image Computing (iMIMIC), 202

Dosimetric feasibility of hypofractionation for metastatic bone/bone marrow lesions from paediatric solid tumours

Background and purpose: The aim of this study was to determine the feasibility of hypofractionated schedules for metastatic bone/bone marrow lesions in children and to investigate dosimetric differences to the healthy surrounding tissues compared to conventional schedules. Methods: 27 paediatric patients (mean age, 7 years) with 50 metastatic bone/bone marrow lesions (n = 26 cranial, n = 24 extra-cranial) from solid primary tumours (neuroblastoma and sarcoma) were included. The PTV was a 2 mm expansion of the GTV. A prescription dose of 36 and 54 Gy EQD2 α / β =10 was used for neuroblastoma and sarcoma lesions, respectively. VMAT plans were optimized for each single lesion using different fractionation schedules: conventional (30/20 fractions, V 95% ≥ 99%, D 0.1cm 3 ≤ 107%) and hypofractionated (15/10/5/3 fractions, V 100% ≥ 95%, D 0.1cm 3 ≤ 120%) . Relative EQD2 differences in OARs D mean between the different schedules were compared. Results: PTV coverage was met for all plans independently of the fractionation schedule and for all lesions (V 95% range 95.5–100%, V 100% range 95.1–100%), with exception of the vertebrae (V 100% range 63.5–91.0%). For most OARs, relative mean reduction in the D mean was seen for the hypofractionated plans compared to the conventional plans, with largest sparing in the 5 fractions (< 43%) followed by the 3 fractions schedule (< 40%). In case of PTV overlap with an OAR, a significant increase in dose for the OAR was observed with hypofractionation. Conclusions: For the majority of the cases, iso-effective plans with hypofractionation were feasible with similar or less dose in the OARs. The most suitable fractionation schedule should be personalised depending on the spatial relationship between the PTV and OARs and the prescription dose

Surface guided radiotherapy practice in paediatric oncology: a survey on behalf of the SIOPE radiation oncology working group

INTRODUCTION: Surface guided radiotherapy (SGRT) is increasingly being implemented to track patient's surface movement and position during radiation therapy. However, limited information is available on the SGRT use in paediatrics. The aim of this double survey was to map SIOPE (European Society for Paediatric Oncology)-affiliated centres using SGRT and to gain information on potential indications, observed, or expected benefits. METHODS: A double online survey was distributed to 246 SIOPE-affiliated radiotherapy (RT) centres. Multiple choices, yes/no, and open answers were included. The first survey (41 questions) was active from February to March 2021. A shortened version (13 questions) was repeated in March 2023 to detect trends in SGRT use within the same community. RESULTS: Respectively, 76/142 (54%) and 28/142 (20%) responding centres used and planned to use SGRT clinically, including 4/34 (12%) new centres since 2021. Among the SGRT users, 33/76 (43%) already applied this technology to paediatric treatments. The main benefits of improved patient comfort, better monitoring of intrafraction motion, and more accurate initial patient set-up expected by future users did not differ from current SGRT-users (P = .893). Among non-SGRT users, the main hurdles to implement SGRT were costs and time for installation. In paediatrics, SGRT is applied to all anatomical sites. CONCLUSION: This work provides information on the practice of SGRT in paediatrics across SIOPE-affiliated RT centres which can serve as a basis for departments when considering the purchase of SGRT systems. ADVANCES IN KNOWLEDGE: Since little information is available in the literature on the use of SGRT in paediatrics, the results of this double survey can serve as a basis for departments treating children when considering the purchase of an SGRT system

Progression-free survival in patients with Ga-68-PSMA-PET-directed SBRT for lymph node oligometastases

BACKGROUND: Prostate cancer oligometastatic disease can be treated using stereotactic body radiotherapy (SBRT) in order to postpone start of systemic treatments such as androgen deprivation therapy (ADT). 68Ga-PSMA-PET/CT imaging allows for diagnosis of oligometastases at lower PSA values. We analysed a cohort of patients with prostate cancer lymph node oligometastases detected on PSMA-PET/CT. MATERIALS AND METHODS: Ninety patients with metachronous oligometastatic prostate cancer received SBRT for 1-3 lymph node metastases diagnosed on 68Ga-PSMA-PET/CT. The primary end point was progression free survival (PFS), with disease progression defined as occurrence of either target lesion progression, new metastatic lesion or biochemical progression. Secondary outcomes were biochemical PFS (BPFS), ADT-free survival (ADT-FS), toxicity and quality of life (QoL). Baseline patient characteristics were tested for association with PFS and a preliminary risk score was created. RESULTS: Median follow-up was 21 months (interquartile range 10-31 months). Median PFS and BPFS were 16 and 21 months, respectively. Median ADT-FS was not reached (73% (95%-CI 62-86%) at 24 months). In multivariable analysis, younger age, higher PSA prior to SBRT and extrapelvic location were associated with shorter PFS. Grade 1 fatigue was the most predominant acute toxicity (34%). Highest grade toxicity was grade 2 for acute and late events. QoL analysis showed mild, transient increase in fatigue at 1-4 weeks after SBRT. CONCLUSION: A median PFS of 16 months was attained after SBRT for patients with PSMA-PET positive oligometastatic lymph nodes from prostate cancer. Higher pre-SBRT PSA, younger age and extrapelvic location were found to be predictors of shorter PFS

Squamous gastric ulceration complicated by gastric stenosis in a foal

A 2-month-old Warmblood colt presented with recurrent colic and regurgitation. Gastroscopy, performed on several occasions, and barium-contrast radiography revealed severe squamous gastric ulceration and stenosis at the level of the margo plicatus. Treatment with omeprazole reduced the extent and severity of the gastric ulcers but did not affect the stenosis. The foal was euthanised because of a poor prognosis, and post-mortem examination confirmed the clinical diagnosis. Severe squamous gastric ulceration, granulation tissue formation and cicatrisation of deep gastric lesions were considered to have caused the stenosis. Gastroduodenal outflow obstruction is a recognised disorder in foals, but stenosis at the level of the margo plicatus has not been reported in foals or adult horses. To the authors' knowledge, this is the first case of severe squamous gastric ulceration, complicated by stenosis at the level of the margo plicatus, in a foal. Although rare, gastric stenosis should be considered in foals suffering recurrent colic and regurgitatio

Radical radiotherapy for paediatric solid tumour metastases:An overview of current European protocols and outcomes of a SIOPE multicenter survey

Purpose/objective: About 20% of children with solid tumours (ST) present with distant metastases (DM). Evidence regarding the use of radical radiotherapy of these DM is sparse and open for personal interpretation. The aim of this survey was to review European protocols and to map current practice regarding the irradiation of DM across SIOPE-affiliated countries. Materials/methods: Radiotherapy guidelines for metastatic sites (bone, brain, distant lymph nodes, lung and liver) in eight European protocols for rhabdomyosarcoma, non-rhabdomyosarcoma soft-tissue sarcoma, Ewing sarcoma, neuroblastoma and renal tumours were reviewed. SIOPE centres irradiating >= 50 children annually were invited to participate in an online survey. Results: Radiotherapy to at least one metastatic site was recommended in all protocols, except for high-risk neuroblastoma. Per protocol, dose prescription varied per site, and information on delineation and treatment planning/delivery was generally missing. Between July and September 2019, 20/27 centres completed the survey. Around 14% of patients were deemed to have DM from ST at diagnosis, of which half were treated with curative intent. A clear cut-off for a maximum number of DM was not used in half of the centres. Regardless of the tumour type and site, conventional radiotherapy regimens were most commonly used to treat DM. When stereotactic radiotherapy was used, a wide range of fractionation regimens were applied. Conclusion: Current radiotherapy guidelines for DM do not allow a consistent approach in a multicentre setting. Prospective (randomised) trials are needed to define the role of radical irradiation of DM from paediatric ST. (C) 2020 The Author(s). Published by Elsevier Ltd

Adverse late health outcomes among children treated with 3D radiotherapy techniques:Study design of the Dutch pediatric 3D-RT study

Background: Adverse late health outcomes after multimodal treatment for pediatric cancer are diverse and of prime interest. Currently available evidence and survivorship care guidelines are largely based on studies addressing side-effects of two dimensional planned radiotherapy. Aims: The Dutch pediatric 3D-planned radiotherapy (3D-RT) study aims to gain insight in the long-term health outcomes among children who had radiotherapy in the 3D era. Here, we describe the study design, data-collection methods, and baseline cohort characteristics. Methods and Results: The 3D-RT study represents an expansion of the Dutch Childhood Cancer Survivor study (DCCSS) LATER cohort, including pediatric cancer patients diagnosed during 2000–2012, who survived at least 5 years after initial diagnosis and 2 years post external beam radiotherapy. Individual cancer treatment parameters were obtained from medical files. A national infrastructure for uniform collection and archival of digital radiotherapy files (Computed Tomography [CT]-scans, delineations, plan, and dose files) was established. Health outcome information, including subsequent tumors, originated from medical records at the LATER outpatient clinics, and national registry-linkage. With a median follow-up of 10.9 (interquartile range [IQR]: 7.9–14.3) years after childhood cancer diagnosis, 711 eligible survivors were identified. The most common cancer types were Hodgkin lymphoma, medulloblastoma, and nephroblastoma. Most survivors received radiotherapy directed to the head/cranium only, the craniospinal axis, or the abdominopelvic region. Conclusion: The 3D-RT study will provide knowledge on the risk of adverse late health outcomes and radiation-associated dose-effect relationships. This information is valuable to guide follow-up care of childhood cancer survivors and to refine future treatment protocols.</p